arXiv subjects

Graeme Henkelman

Publications and source records attributed to Graeme Henkelman.

9 recordsLinked to original sources

arXiv2025

Application-specific machine-learned interatomic potentials: exploring the trade-off between DFT convergence, MLIP expressivity, and computational cost

Machine-learned interatomic potentials (MLIPs) are revolutionizing computational materials science and chemistry by offering an efficient alternative to {\em ab initio} molecular dynamics (MD) simulations. However, fitting high-quality MLIPs remains a challenging, time-consuming, and computationally intensive task where numerous trade-offs have to be considered, e.g., How much and what kind of atomic configurations should be included in the training set? Which level of {\em ab initio} convergence should be used to generate the training set? Which loss function should be used for fitting the MLIP? Which machine learning architecture should be used to train the MLIP? The answers to these questions significantly impact both the computational cost of MLIP training and the accuracy and computational cost of subsequent MLIP MD simulations. In this study, we use a configurationally diverse beryllium dataset and quadratic spectral neighbor analysis potential. We demonstrate that joint optimization of energy versus force weights, training set selection strategies, and convergence settings of the {\em ab initio} reference simulations, as well as model complexity can lead to a significant reduction in the overall computational cost associated with training and evaluating MLIPs. This opens the door to computationally efficient generation of high-quality MLIPs for a range of applications which demand different accuracy versus training and evaluation cost trade-offs.

physics.comp-ph↗

arXiv2025

AlphaNet: Scaling Up Local-frame-based Atomistic Interatomic Potential

Molecular dynamics simulations demand an unprecedented combination of accuracy and scalability to tackle grand challenges in catalysis and materials design. To bridge this gap, we present AlphaNet, a local-frame-based equivariant model that simultaneously improves computational efficiency and predictive precision for interatomic interactions. By constructing equivariant local frames with learnable geometric transitions, AlphaNet encodes atomic environments with enhanced representational capacity, achieving state-of-the-art accuracy in energy and force predictions. Extensive benchmarks on large-scale datasets spanning molecular reactions, crystal stability, and surface catalysis (Matbench Discovery and OC2M) demonstrate its superior performance over existing neural network interatomic potentials while ensuring scalability across diverse system sizes with varying types of interatomic interactions. The synergy of accuracy, efficiency, and transferability positions AlphaNet as a transformative tool for modeling multiscale phenomena, decoding dynamics in catalysis and functional interfaces, with direct implications for accelerating the discovery of complex molecular systems and functional materials.

cs.LG↗

arXiv2023

Atom probe analysis of BaTiO3 enabled by metallic shielding

Atom probe tomography has been raising in prominence as a microscopy and microanalysis technique to gain sub-nanoscale information from technologically-relevant materials. However, the analysis of some functional ceramics, particularly perovskites, has remained challenging with extremely low yield and success rate. This seems particularly problematic for materials with high piezoelectric activity, which may be difficult to express at the low temperatures necessary for satisfactory atom probe analysis. Here, we demonstrate the analysis of commercial BaTiO3 particles embedded in a metallic matrix. Density-functional theory shows that a metallic coating prevents charge penetration of the electrostatic field, and thereby suppresses the associated volume associated change linked to the piezoelectric effect.

cond-mat.mtrl-sci↗

arXiv2021

Atomistic mechanisms of binary alloy surface segregation from nanoseconds to seconds using accelerated dynamics

Although the equilibrium composition of many alloy surfaces is well understood, the rate of transient surface segregation during annealing is not known, despite its crucial effect on alloy corrosion and catalytic reactions occurring on overlapping timescales. In this work, CuNi bimetallic alloys representing (100) surface facets are annealed in vacuum using atomistic simulations to observe the effect of vacancy diffusion on surface separation. We employ multi-timescale methods to sample the early transient, intermediate, and equilibrium states of slab surfaces during the separation process, including standard MD as well as three methods to perform atomistic, long-time dynamics: parallel trajectory splicing (ParSplice), adaptive kinetic Monte Carlo (AKMC), and kinetic Monte Carlo (KMC). From nanosecond (ns) to second timescales, our multiscale computational methodology can observe rare stochastic events not typically seen with standard MD, closing the gap between computational and experimental timescales for surface segregation. Rapid diffusion of a vacancy to the slab is resolved by all four methods in tens of ns. Stochastic re-entry of vacancies into the subsurface, however, is only seen on the microsecond timescale in the two KMC methods. Kinetic vacancy trapping on the surface and its effect on the segregation rate are discussed. The equilibrium composition profile of CuNi after segregation during annealing is estimated to occur on a timescale of seconds as determined by KMC, a result directly comparable to nanoscale experiments.

cond-mat.mtrl-sci↗

arXiv2021

PTCDA molecular monolayer on Pb thin films: An unusual π-electron Kondo system and its interplay with a quantum-confined superconductor

The hybridization of magnetism and superconductivity has been an intriguing playground for correlated electron systems, hosting various novel physical phenomena. Usually, localized d- or f-electrons are central to magnetism. In this study, by placing a PTCDA (3,4,9,10-perylene tetracarboxylic dianhydride) molecular monolayer on ultra-thin Pb films, we built a hybrid magnetism/superconductivity (M/SC) system consisting of only sp electronic levels. The magnetic moments reside in the unpaired molecular orbital originating from interfacial charge-transfers. We reported distinctive tunneling spectroscopic features of such a Kondo screened pi-electron impurity lattice on a superconductor in the regime of TK>>delta suggesting the formation of a two-dimensional bound states band. Moreover, moiré superlattices with tunable twist angle and the quantum confinement in the ultra-thin Pb films provide easy and flexible implementations to tune the interplay between the Kondo physics and the superconductivity, which are rarely present in M/SC hybrid systems.

cond-mat.supr-con↗

arXiv2020

One-dimensional van der Waals heterostructures as efficient metal-free oxygen electrocatalysts

Two-dimensional covalent organic frameworks (2D-COFs) are an emerging family of catalytical materials with well-defined molecular structures. The stacking of 2D nanosheets and large intrinsic bandgaps significantly impair their performance. Here, we report coaxial one-dimensional van der Waals heterostructures (1D vdWHs) comprised of a carbon nanotube (CNT) core and a thickness tunable thienothiophene-pyrene COF shell using a solution based in situ wrapping method. Density functional theory calculations and in-operando and ex-situ spectroscopic analysis show that the carbon-sulfur region in the thienothiophene groups is the active catalytic site. The unique coaxial structure enables controllable n-doping from the CNT core to the COF shell depending on COF shell thickness, which lowers the bandgap and work function of COF. Consequently, the charge transfer barrier between the active catalytic site and adsorbed oxygen intermediates becomes lower, resulting in a dramatic enhancement in their catalytic activity for oxygen redox reactions. It enables a high-performance rechargeable zinc-air battery with a specific capacity of 696 mAh gZn-1 under a high current density of 40 mA cm-2 and excellent cycling stability. 1D vdWHs open the door to create multi-dimensional vdWHs for exploring fundamental physics and chemistry, as well as practical applications in electrochemistry, electronics, photonics, and beyond.

cond-mat.mtrl-sci↗

arXiv2014

First Principles Study of Photo-oxidation Degradation Mechanisms in P3HT for Organic Solar Cells

We present a theoretical study of degradation mechanisms for photoinduced oxidation in organic polymers in the condensed phase, using poly(3-hexylthiophene)(P3HT) as an example. Applying density functional theory with a hybrid density functional and periodic boundary conditions that account for steric effects and permit the modeling of interchain chemical reactions, we investigate reaction pathways that may lead to the oxidation of thiophene backbone as a critical step toward disrupting the polymer conjugation. We calculate energy barriers for reactions of the P3HT backbone with oxidizing agents including hydroxyl radical (OH$\cdot$), hydroperoxide (ROOH), and peroxyl radical (ROO$\cdot$), following a UV-driven radical reaction starting at the $α$-carbon of the alkyl side chain as suggested by infrared (IR) and X-ray photoemission (XPS) spectrosocopy studies. The results strongly suggest that an attack of OH$\cdot$ on sulfur in P3HT is unlikely to be thermodynamically favored. On the other hand, an attack of a peroxyl radical on the side chain on the P3HT backbone may provide low barrier reaction pathways to photodegradation of P3HT and other polymers with side chains. The condensed phase setting is found to qualitatively affect predictions of degradation processes.

cond-mat.mtrl-sci↗

arXiv2014

Interfacial adhesion between graphene and silicon dioxide by density functional theory with van der Waals corrections

Interfacial adhesion between graphene and a SiO2 substrate is studied by density functional theory (DFT) with dispersion corrections. The results demonstrate the van der Waals (vdW) interaction as the predominate mechanism for the graphene/SiO2 interface. It is found that the interaction strength is strongly influenced by changes of the SiO2 surface structures due to surface reactions with water. The adhesion energy is reduced when the reconstructed SiO2 surface is hydroxylated, and further reduced when covered by a monolayer of adsorbed water molecules. Thus, the effect of humidity may help explain the wide variation of adhesion energies measured in recent experiments between graphene and SiO2. Moreover, it is noted that vdW forces are required to accurately model the graphene/SiO2 interface with DFT and that the adhesion energy is underestimated by empirical force fields commonly used in atomistic simulations.

cond-mat.mtrl-sci↗

arXiv2004

Conformational Dependence of a Protein Kinase Phosphate Transfer Reaction

Atomic motions and energetics for a phosphate transfer reaction catalyzed by the cAMP-dependent protein kinase (PKA) are calculated by plane-wave density functional theory, starting from structures of proteins crystallized in both the reactant conformation (RC) and the transition-state conformation (TC). In the TC, we calculate that the reactants and products are nearly isoenergetic with a 0.2 eV barrier; while phosphate transfer is unfavorable by over 1.2 eV in the RC, with an even higher barrier. With the protein in the TC, the motions involved in reaction are small, with only P$_γ$ and the catalytic proton moving more than 0.5 Å. Examination of the structures reveals that in the RC the active site cleft is not completely closed and there is insufficient space for the phosphorylated serine residue in the product state. Together, these observations imply that the phosphate transfer reaction occurs rapidly and reversibly in a particular conformation of the protein, and that the reaction can be gated by changes of a few tenths of an Åin the catalytic site.

physics.chem-ph↗